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comparison BEDTools-Version-2.14.3/src/utils/chromsweep/chromsweep.h @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 chromsweepBed.h
3
4 (c) 2009 - Aaron Quinlan
5 Hall Laboratory
6 Department of Biochemistry and Molecular Genetics
7 University of Virginia
8 aaronquinlan@gmail.com
9
10 Licenced under the GNU General Public License 2.0 license.
11 ******************************************************************************/
12 #ifndef CHROMSWEEP_H
13 #define CHROMSWEEP_H
14
15 #include "bedFile.h"
16 #include <vector>
17 #include <queue>
18 #include <iostream>
19 #include <fstream>
20 #include <stdlib.h>
21 using namespace std;
22
23
24
25 class ChromSweep {
26
27 // public interface.
28 public:
29
30 // A is the query and B is the database
31
32 // constructor using existing BedFile pointers
33 ChromSweep(BedFile *bedA, BedFile *bedB, bool sameStrand = false, bool diffStrand = false);
34
35 // constructor using filenames
36 ChromSweep(string &bedAFile, string &bedBFile);
37
38 // destructor
39 ~ChromSweep(void);
40
41 // loads next (a pair) with the current query and it's overlaps
42 // next.first is the current query interval
43 // next.second is a vector of the current query's hits.
44 // returns true if overlap
45 bool Next(pair<BED, vector<BED> > &next);
46
47 // Usage:
48 // ChromSweep sweep = ChromSweep(_bedA, _bedB);
49 // pair<BED, vector<BED> > hit_set;
50 // while (sweep.Next(hit_set))
51 // {
52 // // magic happens here!
53 // processHits(hit_set.first, hit_set.second);
54 // }
55
56 // private variables.
57 private:
58
59 // instances of a bed file class.
60 BedFile *_bedA, *_bedB;
61 // do we care about strandedness.
62 bool _sameStrand, _diffStrand;
63 // a cache of still active features from the database file
64 vector<BED> _cache;
65 // the set of hits in the database for the current query
66 vector<BED> _hits;
67 // a queue from which we retrieve overlap results. used by Next()
68 queue< pair<BED, vector<BED> > > _results;
69 BED _nullBed;
70 // an empty BED vector for returning no hits for a given query
71 vector<BED> _no_hits;
72 // the current query and db features.
73 BED _curr_qy, _curr_db;
74 // a cache of the current chrom from the query. used to handle chrom changes.
75 string _curr_chrom;
76 // the current line status in the database and query files
77 BedLineStatus _qy_status, _db_status;
78 // the current line numbers in the database and query files
79 int _qy_lineNum, _db_lineNum;
80
81 // private methods.
82 private:
83
84 void ScanCache();
85 bool ChromChange();
86 bool IsValidHit(const BED &query, const BED &db);
87 };
88
89 #endif /* CHROMSWEEP_H */